Bam (p.biocaml.0.11.2.doc.biocaml.ez.Biocaml

include module type of struct include Biocaml_unix.Bam end

A BAM file is composed of a header and a list of alignment records. The datatypes used in this module are based on those defined in the Sam module.

Sourcemodule Header = Biocaml_unix.Bam.Header

BAM header files contain a plain text SAM header, plus additional information related to the encoding of the file.

Sourcetype alignment = Biocaml_unix.Sam.alignment

Sourcemodule Alignment0 = Biocaml_unix.Bam.Alignment0

Representation of partially parsed alignments. When traversing a BAM file for a specific calculation, it may be that only some fields of the alignment records are actually used. In that case, it can be significantly faster to use this representation. As a downside, some encoding errors in the BAM file can go unnoticed.

Source

val read0 : 
  Core.In_channel.t ->
  (Header.t * Alignment0.t Core.Or_error.t Stream.t) Core.Or_error.t

read0 ic returns an error if a valid header cannot be read from ic or a pair containing a header and a stream of possibly errored (partially parsed) alignments. The stream stops after the first error.

Sourceval write0 : Header.t -> Alignment0.t Stream.t -> Core.Out_channel.t -> unit

write0 h xs oc writes the header h and (partially parsed) alignments xs to oc.

Source

val read : 
  Core.In_channel.t ->
  (Header.t * alignment Core.Or_error.t Stream.t) Core.Or_error.t

read ic returns an error if a valid header cannot be read from ic or a pair containing a header and a stream of possibly errored alignments. The stream stops after the first error.

Source

val write : 
  Header.t ->
  alignment Stream.t ->
  Core.Out_channel.t ->
  unit Core.Or_error.t

write h xs oc writes the header h and the alignments xs to oc.

Low-level access

Sourceval read_header : Biocaml_unix.Bgzf.in_channel -> Header.t Core.Or_error.t

Source

val read_alignment : 
  Biocaml_unix.Bgzf.in_channel ->
  Alignment0.t Core.Or_error.t option

Source

val read_alignment_stream : 
  Biocaml_unix.Bgzf.in_channel ->
  Alignment0.t Core.Or_error.t Stream.t

Source

val with_file : 
  string ->
  f:(Header.t -> alignment CFStream.Stream.t -> 'a) ->
  'a

Source

val with_file0 : 
  string ->
  f:(Header.t -> Alignment0.t CFStream.Stream.t -> 'a) ->
  'a